5-25760570-G-T

Position:

• chr5-25760570-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.632 in 152,062 control chromosomes in the GnomAD database, including 32,703 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (32703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96096 AN: 151944 Hom.: 32691 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.632 AC: 96130 AN: 152062 Hom.: 32703 Cov.: 33 AF XY: 0.628 AC XY: 46691 AN XY: 74332

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.647

Alfa AF: 0.745 Hom.: 97114

Bravo AF: 0.620

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7727656; hg19: chr5-25760679;